Telomeric repeats act as nucleosome-disfavouring sequences in vivo

Yuichi Ichikawa,Yoshifumi Nishimura,Hitoshi Kurumizaka,Nobuyuki Morohashi,Mitsuhiro Shimizu

doi:10.1093/nar/gkt1006

Yuichi Ichikawa, Yoshifumi Nishimura + Show 3 more

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https://doi.org/10.1093/nar/gkt1006

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Abstract

Telomeric DNAs consist of tandem repeats of G-clusters such as TTAGGG and TG1-3, which are the human and yeast repeat sequences, respectively. In the yeast Saccharomyces cerevisiae, the telomeric repeats are non-nucleosomal, whereas in humans, they are organized in tightly packaged nucleosomes. However, previous in vitro studies revealed that the binding affinities of human and yeast telomeric repeat sequences to histone octamers in vitro were similar, which is apparently inconsistent with the differences in the human and yeast telomeric chromatin structures. To further investigate the relationship between telomeric sequences and chromatin structure, we examined the effect of telomeric repeats on the formation of positioned nucleosomes in vivo by indirect end-label mapping, primer extension mapping and nucleosome repeat analyses, using a defined minichromosome in yeast cells. We found that the human and yeast telomeric repeat sequences both disfavour nucleosome assembly and alter nucleosome positioning in the yeast minichromosome. We further demonstrated that the G-clusters in the telomeric repeats are required for the nucleosome-disfavouring properties. Thus, our results suggest that this inherent structural feature of the telomeric repeat sequences is involved in the functional dynamics of the telomeric chromatin structure.

Highlights

In eukaryotic chromosomes, the nucleosome is a fundamental structural and functional unit, composed of a histone octamer and 146 bp of DNA [1,2]
Telomeric DNAs consist of tandem repeats of 5–8 bp
In lower eukaryotes, the telomeric tandem repeats are organized within a non-nucleosomal chromatin structure, in which they are covered by an array of Rap1 and other protein components [3,4,7]

Summary

Introduction

The nucleosome is a fundamental structural and functional unit, composed of a histone octamer (two molecules each of histones H2A, H2B, H3 and H4) and 146 bp of DNA [1,2]. There are characteristic differences in telomere organization between lower and higher eukaryotes [3,4,5]. The lengths of the telomeric repetitive elements are relatively short, and are typically a few hundred base pairs in yeasts and other lower eukaryotes. The repetitive elements in higher eukaryotes are several thousand base pairs long, and their lengths are highly variable. In lower eukaryotes, the telomeric tandem repeats are organized within a non-nucleosomal chromatin structure, in which they are covered by an array of Rap and other protein components [3,4,7]. The organization of the chromatin structures in the telomeric repeat regions is remarkably different between lower and higher eukaryotes

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